Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_diversity_alpha-group-significance.xml @ 4:71f124e02000 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
8 qiime diversity alpha-group-significance 8 qiime diversity alpha-group-significance
9 9
10 --i-alpha-diversity=$ialphadiversity 10 --i-alpha-diversity=$ialphadiversity
11 11
12 12
13 #if $input_files_mmetadatafile:
13 #def list_dict_to_string(list_dict): 14 #def list_dict_to_string(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]: 16 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 #end for 18 #end for
18 #return $file_list 19 #return $file_list
19 #end def 20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if
20 23
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 24
23 --o-visualization=ovisualization 25 --o-visualization=ovisualization
24 ; 26 ;
25 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
26 && cp -r out/* '$ovisualization.files_path' 28 && cp -r out/* '$ovisualization.files_path'
27 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
28 ]]></command> 30 ]]></command>
29 <inputs> 31 <inputs>
30 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/> 32 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
31 33
32 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
33 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
34 </repeat> 36 </repeat>
35 </inputs> 37 </inputs>
36 <outputs> 38 <outputs>
37 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
38 </outputs> 40 </outputs>
39 <help><![CDATA[ 41 <help><![CDATA[
40 Beta diversity group significance 42 Alpha diversity comparisons
41 #################################
42 43
43 Determine whether groups of samples are significantly different from one 44 Visually and statistically compare groups of alpha diversity values.
44 another using a permutation-based statistical test.
45 45
46 Parameters 46 Parameters
47 ---------- 47 ----------
48 distance_matrix : DistanceMatrix 48 alpha_diversity : SampleData[AlphaDiversity]
49 Matrix of distances between pairs of samples. 49 Vector of alpha diversity values by sample.
50 metadata : MetadataColumn[Categorical] 50 metadata : Metadata
51 Categorical sample metadata column. 51 The sample metadata.
52 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
53 The group significance test to be applied.
54 pairwise : Bool, optional
55 Perform pairwise tests between all pairs of groups in addition to the
56 test across all groups. This can be very slow if there are a lot of
57 groups in the metadata column.
58 permutations : Int, optional
59 The number of permutations to be run when computing p-values.
60 52
61 Returns 53 Returns
62 ------- 54 -------
63 visualization : Visualization 55 visualization : Visualization
64 ]]></help> 56 ]]></help>